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Supplementary Figure 3 7.0 Col Kas-1 Line FTH1A 8.4 F3PII3 8.9 F26H11 ATQ1 T9I22 PLS8 F26B6-B 9.6 F27L4 9.81 F27D4 9.92 9.96 10.12 10.14 10.2 11.1 0.5 Mb T1D16 Col % RGR 83.3 101 227 93.5 75.9 132 90 375 70.9 300 84.1 297 574 609 1.2 76.32 70.3 578 0 289 535 1.12 8.0 L128 20.6 Supplementary Figure 3. Fine mapping of ATQ1. Genotype and As(V) tolerance phenotype, determined as %RGR, in selected lines from a NIL128 x Col gl-1 (Col) F 2 population. The recombination breakpoints at the FTH1A and T1D16 interval are depicted; Kas-1 (red), Col gl-1 (Col; green). ATQ1 is located between markers F26H11 and T9I22.

Supplementary Figure 5 Supplementary Figure 5. Phylogenetic relationships among rhodanase proteins. Neighbor-Joining tree including 49 sequences from 31 plant species selected by the highest homology to the rhodanase encoded by AtARQ1 gene (At2g21045). They correspond to three Arabidopsis thaliana proteins (AtARQ1, At5g66170 and At5g66040), a pair of proteins from each of 16 plant species (indicated with numbers 1 or 2 close to species names) and a single protein from each of 14 other plants. In addition, 9 ACR2 like proteins are included from protista, algae and plants. The bootstrap consensus tree inferred from 10000 replicates is taken to represent the evolutionary history of the taxa analyzed. The evolutionary distances were computed using the Poisson correction method and are in the units of the number of amino acid substitutions per site. The analysis involved 58 amino acid sequences. All ambiguous positions were removed for each sequence pair. There were a total of 200 positions in the final dataset. Evolutionary analysis was conducted in MEGA6 51. Sequence accession numbers are: Arabidopsis thaliana AtARQ1 (At2g21045): AAP37665; Arabidopsis thaliana AT5G66040: AAN38701; Arabidopsis thaliana AT5G66170: AAM10268; Arabidopsis lyrata 1: 899363; Arabidopsis lyrata 2: 496998; Thellungiella halophila 1: Thhalv10022902m; Thellungiella halophila 1: Thhalv10005118m; Capsella rubella 1: Carubv10025520m; Capsella rubella 2: Carubv10028451m; Brassica rapa 1: Bra002059; Brassica rapa 2: Bra012056; Carica papaya 1: supercontig 37.162; Carica papaya 2: supercontig 6.271; Cucumis sativus 1: CucsArabidopsis234370; Cucumis sativus 2: CucsArabidopsis044010; Prunus persica 1: ppa024101; Prunus persica 2: ppa011976; Malus domestica: MDP0000433388; Mimulus guttatus: mgv1a018856; Vitis vinifera 1: GSVIVG01018758001; Vitis vinifera 2: GSVIVG01018760001; Manihot esculenta: cassava4.1 017198; Citrus sinensis 1: orange1.1g041947m; Citrus sinensis 2: orange1.1g032621m; Citrus clementina: Ciclev10026690m; Setaria italica: Si031418m; Aquilegia coerulea: Aquca_006_00217.1; Eucalyptus grandis 1: Eucgr.E01127.1; Eucalyptus grandis 2: Eucgr.L00782.1; Solanum tuberosum: PGSC0003DMG400003573; Solanum lycopersicum: Solyc02g083730.2.1; Medicago truncatula 1: Medtr2g017630.1; Medicago truncatula 2: Medtr8g075420.1; Glycine max 1: Glyma12g02040.1; Glycine max 2: Glyma01g37010.1; Phaseouls vulgaris: Phvul.011G020400; Gossypium raimondii 1: Gorai.013G141700.1; Gossypium raimondii 2: Gorai.007G049000.3; Populus trichocarpa 1: Potri.014G131300.1; Populus trichocarpa 2: Potri.005G111200.2; Fragaria vesca: mrna24304.1-v1.0-hybrid; Theobroma cacao: Thecc1EG032968t1; Brachypodium distachyon: Bradi3g00377.1; Oriza sativa 1: Os04g17660.1; Oriza sativa 2: Os02g01220.1; Panicum virgatum: Pavirv00038676m; Sorghum bicolor 1: Sb06g003340; Sorghum bicolor 2: Sb04g000410; Zea mays: AC204711.3 FG003; Saccharomyces cerevisae ACR2: NP 015526; Leishmania major ACR2: AAS73185; Gossypium arboreum ACR2: AW666950; Oriza sativa ACR2: BE039986; Chlamydomonas reinhardtii ACR2: AW661050; Arabidopsis thaliana ACR2 AT5G03455: AAO39886; Pteris vittata ACR2: ADP20951; Holcus lanatus ACR2: AY704470; Zea mays ACR2: AY108501.

Supplementary Figure 7 a Col-0 ATGTATACATATTCTCTCCTCAACCTTTCTCATTGCAGAAGACAAACCAGAAAGAAAAGAAAAACAGATCACACCGAAGGCTTTCTCATGGAGGAAACAA Kas-1 ATG-ATACATATCCTCTCTTCAACCTTTCTCATTGCAAAAGACATACCAGAA-----AGAAAAACAGATCAAACCGAAGGCTTTCTCATGGAGGAAACAA Col-0 AACCAAAGACCGTTGAAGATGTTGAGACCGTTGATGTTTATACAGCTAAAGGCTTTCTTAGTACTGGTCACCGATATCTCGACGTAAGGACAAATGAAGA Kas-1 AACCAAAGACCGTTGAAGATGTTGAGACCGTTGATATTTATACAGCTAAAGGCTTTCTTAGTACTGGTCACCGATATCTCGACGTAAGGACAAGTGAAGA Col-0 ATTTGCCAAGAGTCATGTTGAGGAGGCTTTGAACATTCCTTATATGTTCAAAACAGATGAAGGTAGGGTTATAAATCCTGATTTCCTTTCTCAAGTGGCA Kas-1 ATTTGCCAAGAGTCATGTTGAGGAGGCTTTGAACATTCCTTATATGTTCCAAACAGATGAAGGTAGGGTTATAAATCCTGATTTCCTTTCTCAAGTGGCA Col-0 TCGGTTTGCAAGAAAGATGAACATTTGATCGTGGCTTGTAACGCTGGAGGAAGAGGAAGTCGTGCTTGCGTTGATCTTCTTAACGAGGGGTACGACCATG Kas-1 TCGGTTTGCAAGAAAGATGAACATTTGATCGTGGCTTGTAACGCTGGAGGAAGAGGAAGTCGTGCTTGCGTTGATCTTCTCAACGAGGGGTACGACCATG * Col-0 TGGCTAACATGGGGGGAGGCTACTCGGCTTGGGTTGACGCTGGATTCGCCGGGGACAAACCCCCGGAAGACCTCAAGATTGCTTGCAAGTTCAGGCCAAA Kas-1 TGGCTAACATGGGGGGAGGCTACTCGGCTTGGGTTGACGCTGGATTCGCCGGGGACAAACCCCCGGGAGACCTCAAGATTGCTTGCAAGTTCAGGCCAAA Col-0 GGAAAACTAA Kas-1 GGAAAACTAA b Bur-0 Chi-0 Col-0 Lm-2 Kz-2 Bay-0 Pi-0 Yeg-1 Sav-0 Ct-1 Fuk-0 Es-0 A.lyrata Kas-1 Fei-0 Edi-0 Ll-0 Ri-0 Shak-0 Tsu-1 kondara c 0.01 Supplementary Figure 7. Col-0 and Kas-1 define two haplogroups for the AtARQ1 gene in Arabidopsis thaliana. (a) Nucleotide diversity between Col-0 and Kas-1 AtARQ1 coding sequence. Compensatory indels and single nucleotide polymorphisms in Col-0 (green) and Kas-1 (red). *synonymous mutation. (b) Phylogram constructed using Clustal-W of AtARQ1 coding sequences from 20 Arabidopsis accessions and Arabidopsis lyrata. (c) Geographic distribution of Arabidopsis accessions used, classified by Col-0 or Kas-1 haplogroup.

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